There are some workarounds, like the one described by [b]Axxer [/b]in the thread:
to map the hide funktion as follows:
"NOT <right joystick up> AND NOT <right joystick left> AND
NOT <right joystick right> AND NOT <right joystick down>.
That way, unless you specifically move the cursor, it won't be visible
in screen"

This works fine on the first sight, but when you move the stick from left to right, then the IR diappears for a moment - since in the transition from left to right there is state where it is not left and not right (hope you geht the logic here)

My solution to this was to map hide to "NOT RB" on the pad - this way you have to press rb to "activate" the IR, do some pointing stuff, and then let go of RB, which lets the IR diappear again.
But this wastes one button, and is kind of awkward to use.

Would it be possible to introduce a feature to dolphin like "hide IR after x seconds of inactivity" ?
This would realy help out the gamepad users

Can someone pass this request to the developers - or can tell me the official way to do this?

Ok, here's what you do. Go here. https://code.google.com/p/dolphin-emu/issues/list and make an issue. Request a "toggle" function. That should give you what you need and be a lot easier for the developers than a "hide IR after X period" feature. I can't promise it will be responded to quickly though; Jasper left so there is only Billiard to work on this kind of thing, and he's been busy. But at least when it's on googlecode they'll be aware of it.